Using version 0.3.22rc2 on Windows:

I got 0.02 from the faucet. I had over 500 confirmations by the time I tried to send it on. I sent 0.01 and the small transaction dialog popped up saying that I would need to pay the fee of 0.0005. I accepted by pressing yes and when the transaction posted it took 0.02 from my balance leaving me with 0.00 instead of 0.0095, which is what I should have been left with if 0.0005 had actually been taken from me.

This is the transaction: http://blockexplorer.com/tx/223fb42799f90eaafe621a188c3361a2385247893d85b7ddbf02f145b402d811

You will notice the amount of the transaction is 0.02 instead of 0.0105

Also, possibly related to this bug is the fact that all forms on the interface are hard coded to only accept 0.00 and no more decimal places beyond two. This seems like it could cause problems sending amounts as small as even the alleged new transaction fee of 0.0005.